Evolution machine speeds up search for better bugs

If humans want to persuade microbes to produce vast quantities of fuels or pharmaceuticals, we may need to give evolution a helping hand. A new genome engineering machine that tweaks dozens of genes to create billions of unique strains in a few days does just that.

“The general motivation behind what we’re trying to do is develop a set of techniques that will allow us to write into the genome of any organism with the same ease that we are able to read from the genome by DNA sequencing,” he adds.

Cheap and fast

Traditionally, genetic engineers tackle one gene at a time, systematically mutating its letters to achieve a particular effect, such as higher protein yield or stability. But since many commercially useful chemicals rely on networks of dozens of genes, it becomes difficult, bordering on impossible, to systematically mutate each gene in a complex pathway.

Advertisement

The American chemicals firm DuPont, for instance, spent nearly seven years and hundreds of millions of dollars to identify 20 genetic changes that optimise microbes to produce a chemical used as a commercial solvent called 1,3-propanediol, Isaacs and Wang say.

By contrast, the new approach, which is called multiplex automated genome engineering or MAGE, can create hundreds or thousands of mutations in a few days at a cost of a few thousand dollars.

Red bugs

To demonstrate MAGE, the researchers engineered Escherichia coli that churn out five times as much of a chemical called lycopene than their forbearers. Lycopene is an antioxidant abundant in tomatoes that is related to compounds used to fight cancer and malaria.

With at least 20 genes known to affect lycopene production, conventional genetic engineering techniques that re-write a gene or a part of gene at a time wouldn’t suffice.

In many cases, a mutation in one gene that stymies production can be offset by a mutation in another gene. Occasionally, these double mutants produce a chemical more efficiently than a strain with no changes.

But instead of trying to directly create double-mutants, Wang and Farren’s approach produced hundreds, even thousands of mutations simultaneously, resulting in billions of different strains. Because lycopene colours cells red, the researchers simply selected the brightest bacteria.

“There might be cells out there that may have these properties, but what we’re trying to do is accelerate this process to find the specific traits we’re interested in,” Wang says.

Powerful tool

MAGE relies on the tendency of cells to incorporate little bits of laboratory made DNA into their dividing chromosomes. Researchers can customise those bits so they modify specific genes and even parts of genes.

This lets scientists exert as much or as little control over the mutations as they see fit. “A lot of times when you’re doing engineering, you have a very specific objective&colon; ‘I need to make this change’,” Wang says. “For a lot of what we do in terms of genetic engineering, we don’t necessarily know the solution.”

Engineering vitamin-producing bacteria isn’t the only use for the new technique, Isaacs says. “It will immediately decrease the time it will take to improve the efficiency and production of virtually any compound that’s generated, right now, in E. coli and looking beyond into other types of organisms as well.”

The team is planning to adapt the technique to yeast soon, and plant and animal cells should also prove amenable to MAGE, they say.

Currently, the researchers are teaming up with biofuels and chemical manufacturers in hopes of creating blockbuster strains in the lab that could eventually be used on an industrial scale.

“I … look at this paper and think, that’s really cool and it’s a stepping stone,” says Andy Ellington, a biochemist at the University of Texas in Austin. By mapping out the myriad mutations that endow bacteria with useful traits, such as bio-fuel production, researchers will eventually learn to predict the effects of mutations and create their own custom strains.

“Gosh, when it becomes cheap to make E. coli from scratch, why won’t we do that,” Ellington says.